Anemia is a prevalent circulatory system illness that is severely harmful to patients. The development of novel oral delivery systems for iron compounds with enhanced biopharmaceutical properties is vital considering the severe side effects associated with oral medication use. We believe incorporating iron compounds to polymethylsilsesquioxane hydrogels is a promising approach. According to previously published materials, such a system should have great biocompatibility and a capacity for iron compounds, and it may be able to release contents into the intestine. This study investigated polymethysilsesquioxane hydrogels with varying silicate unit concentrations. Potential iron-containing medicines were iron(III) chloride (FeCl3∙6H2O)) and iron(II) D-gluconate. All hydrogels were found to have nearly 100% sorption activity for a saturated solution of FeCl3∙6H2O (0.27 M) during the experiment, but only around 30% sorption capacity was found for a saturated solution of D-gluconate (0.24 M). A specific field of study was the distribution of iron atoms within hydrogels. It has been established that the largest regions devoid of iron atoms are observed in a hydrogel with a maximum quantity of inorganic units. The outcomes provide opportunities for the precise engineering of polymer matrix structures for iron compound delivery.